7. Project Summary/Abstract Long-Term Objectives The broad goals of this project are to (1) evaluate the effects of rare and common variation in protein-coding and non-coding gene regions, and regulatory intergenic regions on alcohol and tobacco use phenotypes; (2) test for differential DNA methylation in the context of current alcohol and tobacco use; and (3) investigate the relationship between regulatory sequence variation and DNA methylation and their combined effects on alcohol and tobacco use and dependence. Given the substantial shared genetic etiology for alcohol and tobacco use, the long-term career objective is to develop a program of research that informs prevention and treatment strategies by characterizing the pathophysiological processes that contribute to these traits. Specific Aims There are two primary research aims of this proposal. The first aim focuses on regions of protein-coding and non-coding DNA in order to test the ability of different prioritization and grouping methods to inform genetic association studies of alcohol and tobacco use and dependence. Prioritization methods will include the use of bioinformatics tools to select and assign weights to likely causal rare and common variants within genes and regions susceptible to DNA methylation. These weights will be incorporated into set-based analyses that combine rare and common variants to test for association with alcohol and tobacco use phenotypes. The second aim will evaluate the ability of these prioritization and set-based analytic methods to inform the analysis of DNA methylation microarray data. Specifically, the focus of this aim is to test for epigenetic mediation of genetic risk to determine the extent to which DNA sequence variants in the region are related to level of methylation in the prediction of alcohol and tobacco use and dependence. Analyses will be conducted using whole-genome sequencing and DNA methylation data from a family-based study of alcohol dependence susceptibility. During the period of the award, training will be obtained via (1) coursework, (2) attendance at didactic workshops, and (3) meetings with expert consultants in advanced statistical genetics and DNA methylation methods and analysis. Significance Results from this project will inform molecular genetic studies on the etiology and development of alcohol and tobacco use and dependence. The increasing availability of whole-genome sequence and epigenetic data poses a computational and theoretical challenge for research on complex traits, particularly in the interpretation of the vast extent of rare and common non-coding variation and epigenetic processes in these regions. Thus, results from this project will advance informatics approaches to the study of such traits and our understanding of biological contributions to the risk for substance use disorders.